To me, it always seemed clear that Revan abandoned HK-47 when he abandoned everyone else. Bastila and Carth reluctantly but willingly agreed to stay behind, Canderous was given orders to assemble the Mandalorians, Juhani and Jolee presumably rejoined the Jedi Order to prepare them for Revan's return, and T3-M4 was left behind and tried to help. In my mind, HK refused to obey Revan's command to stay behind, so Revan disabled and dismantled him to keep him from following. I assume he had to do something similar with Zalbaar, who's live debt would have obligated him to follow as well - either that, or he went with Revan as well. Mission might have gone with them, but it's likely she was left behind somewhere as well, possibly in the care of Carth/Bastila.